2018
DOI: 10.1107/s2059798318002425
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ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps

Abstract: ISOLDE is an interactive molecular-dynamics environment for rebuilding models against experimental cryo-EM or crystallographic maps. Analysis of its results reinforces the need for great care when validating models built into low-resolution data.

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Cited by 1,266 publications
(1,101 citation statements)
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References 46 publications
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“…The C1 RBD "up" reconstruction was sharpened 160 in cryoSPARC, and the 3D reconstruction with C3 symmetry was subjected to local B-factor 161 sharpening using LocalDeBlur (33). Models were built in Coot, before being iteratively refined 162 in both Phenix and ISOLDE (34)(35)(36). Some of the data processing and refinement software was 163 curated by SBGrid (37).…”
Section: Cryo-em Data Processing 157mentioning
confidence: 99%
“…The C1 RBD "up" reconstruction was sharpened 160 in cryoSPARC, and the 3D reconstruction with C3 symmetry was subjected to local B-factor 161 sharpening using LocalDeBlur (33). Models were built in Coot, before being iteratively refined 162 in both Phenix and ISOLDE (34)(35)(36). Some of the data processing and refinement software was 163 curated by SBGrid (37).…”
Section: Cryo-em Data Processing 157mentioning
confidence: 99%
“…The atomic model was refined against a half-map using Phenix.real_space_refine (Afonine et al, 2018a) and Rosetta . To improve the geometry of the atomic model, molecular dynamics-assisted model building was carried out in ChimeraX (Goddard et al, 2018) using the ISOLDE tool (Croll, 2018). The other half-map was used for generating model statistics.…”
Section: S-protein Ecto Domain Cryo-em Model Buildingmentioning
confidence: 99%
“…Maps of large systems at lower resolutions (~3 Angstroms) from cryoEM can require extensive interactive refinement because more errors are present. The ChimeraX tool ISOLDE 19 , developed by Tristan Croll, enables corrections and makes use of interactive molecular dynamics to maintain correct bonded geometry, minimize clashes, and move atoms into density. It also computes and displays 3D indicators for poor backbone geometry and bond angles.…”
Section: Resultsmentioning
confidence: 99%